// BA2.h
struct Gene
{
  string g1;
  string g2;
};

struct Indiv
{
  std::vector<Gene> genotypes;  // vector of maternal and paternal genotypes
  string sampledPopulation;        // population sampled from
  string assignedPopulation;       // population assigned to
  string label;                 // label for individual
};

class Parameters
{
 public:
  Parameters();
  string outfile;
  long int MCMCreps;
  long int MCMCthin;
  string fileFormat;
  vector<string> alist;
};

void DataSummary(Parameters pvalues);
int TranslateCommand(string cmd);
void PrintBanner();
void PrintCommands();
void ReadData(ifstream &infile, Parameters &pvalues);
void PrintParameters(Parameters pvalues);
int SetParameters(Parameters &pvalues);
void PrintData();
void GetAlleleCounts();
void PrintAlleleCounts();
